It is working. The error was clerical. Thank you for your time. On Tue, Mar 29, 2011 at 10:52 AM, Sai Pooja <saipo...@gmail.com> wrote:
> > > On Mon, Mar 28, 2011 at 6:39 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > >> On 29/03/2011 4:54 AM, Sai Pooja wrote: >> >> There was a typo in the mail: >> E_protein-protein = Potential - E_water-water - E_protein-water >> >> On Mon, Mar 28, 2011 at 11:55 AM, Sai Pooja <saipo...@gmail.com> wrote: >> >>> Hi, >>> >>> I have tried to implement a variant of Replica exchange called REST >>> using gromacs. In REST, the potential energy is scaled in the following >>> manner: >>> >>> For the nth replica: >>> >>> E_n = E_protein-protein + a_n * E_protein-water + b_n * E_water-water >>> >>> I used tables to implement this. Separate tables for the three >>> components were generated with the corresponding scaled potentials. Then for >>> replica exchange I use gromacs to run MD for 1ps then extract the Energy >>> corresponding to the three components using g-energy and exchange replicas >>> based on the acceptance criteria outlined in the paper. >>> >>> E_water-water = LJ_water-water + Coulomb_water-water >>> E_protein-water = LJ_protein-water + Coulomb_protein-water >>> E_protein-protein = Potential - E_protein-protein - E_protein-water >>> >>> Is there some obvious error in this implementation? I use CHARMM >>> forcefield with tip3p water and alanine dipeptide. The paper uses OPLS-AA >>> with tip4p and is able to use 3 replicas -300k, 420k, 600k. I am not able to >>> reproduce these results i.e. the same acceptance ratio with 3 replicas. 5 >>> replicas gives something close to the desired acceptance ratio. >>> >> >> The exchange ratio depends on the overlap integral of the distributions of >> the potential energy. To have a chance of reproducing their work, you need >> to use similar numbers of degrees of freedom (i.e. number of atoms) so that >> the ratio of width/average of your distributions is similar. >> >> > I have almost the same no. of molecules in the system (503 in my simulation > vs 512 in the paper). I change the combination rule to '1' in the > forcefield.itp file, convert sigma and epsilon to C6 and C12 in ffnonbonded > files, scale the epsilon according to the potential energy scaling for LJ > potential and use tables with scaled coulomb interactions. User and Cutoff > are specified respectively for Coulomb and Vdw interactions in the mdp file. > > I guess I dont need convert sigma and epsilon to C6 and C12 since I am not > using tables for the LJ potential. However, since the combination rule and > the C6, C12 values are consistent, that shouldnt be a problem? > > Mark >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > Quaerendo Invenietis-Seek and you shall discover. > -- Quaerendo Invenietis-Seek and you shall discover.
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